7QXT

ATAD2 in complex with FragLite10


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DAI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.191α = 90
b = 81.191β = 90
c = 134.966γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.979DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5170.311000.1750.1830.0540.9976.919.441986
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.511.549.56910.5984.4660.2399.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3DAI1.5170.3141877210499.8260.2240.22180.255845.639
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.8170.9081.817-5.894
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.018
r_dihedral_angle_3_deg16.519
r_dihedral_angle_4_deg15.875
r_lrange_it11.109
r_lrange_other11.106
r_scangle_it9.098
r_scangle_other9.04
r_scbond_it6.048
r_scbond_other6.002
r_mcangle_it5.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.018
r_dihedral_angle_3_deg16.519
r_dihedral_angle_4_deg15.875
r_lrange_it11.109
r_lrange_other11.106
r_scangle_it9.098
r_scangle_other9.04
r_scbond_it6.048
r_scbond_other6.002
r_mcangle_it5.222
r_mcangle_other5.219
r_dihedral_angle_1_deg5.106
r_mcbond_it4.221
r_mcbond_other4.219
r_angle_refined_deg1.687
r_angle_other_deg1.476
r_xyhbond_nbd_refined0.276
r_symmetry_xyhbond_nbd_refined0.253
r_nbd_other0.232
r_nbd_refined0.212
r_symmetry_nbd_refined0.189
r_symmetry_nbd_other0.178
r_nbtor_refined0.172
r_symmetry_xyhbond_nbd_other0.142
r_xyhbond_nbd_other0.118
r_chiral_restr0.086
r_symmetry_nbtor_other0.082
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
xia2data scaling
PHASERphasing